I have data from three tumor samples from the same patient at different stages. The samples are derived from FFPE sections, and they underwent exome sequencing.
I used CNVkit to calculate the copy number ratio and segment the genome with parameters -m cbs -t 1e-4 --drop-low-coverage --drop-outliers 5.
I noticed that I have copy number gain or loss throughout the entire genome, and when I plot the distribution of the log2 copy number ratio I get two peaks, above and below log2==0 (I would expect many segments to have log2==0). Is it possible that the log2 values are shifted in some way from log2==0?
I am also attaching plots from BubbleTree